LSF dependencies removed. Correction of sql statement to get the list of cores.

misc-scripts/alternative_splicing/as_event_computations.sh

@@ -89,9 +89,9 @@ then
       ## Find a core database for this species on the specified server.
 	  if [[ -n "$password" && $password != "" ]]
 	  then
-				core=`mysql -h ${host} -P ${port} -u ${user} -p ${password} -s --skip-column-names -e "show databases like '${species}_core_%'"`
+				db=`mysql -h${host} -P${port} -u${user} -p${password} -s --skip-column-names -e "show databases like '${species}\_core\_%'"`
 	  else
-				core=`mysql -h${host} -P${port} -u${user} -s --skip-column-names -e "show databases like '${species}_core_%'"`
+				db=`mysql -h${host} -P${port} -u${user} -s --skip-column-names -e "show databases like '${species}\_core\_%'"`
 	  fi
     else
 				echo "Species or/and database name are required." ;
@@ -99,7 +99,7 @@ then
 				exit 1;
     fi
   else
-			core=${db};
+			echo "Using ${db} as core database.";
   fi
 else
 		echo "Hostname and username are required."
@@ -111,7 +111,7 @@ fi
 
 y=0;
 
-for X in ${core}
+for X in ${db}
 do
 		y=$[$y+1];
 done
@@ -126,31 +126,37 @@ fi
 if [[ ${y} -gt 1 ]]
 then
 		echo "Check your parameters, there are ${y} databases matching species '${species}':";
-		echo "$core";
+		echo "${db}";
 		exit 1;
 fi
 
+echo "Using ${db} as core database.";
 
 # Otherwise, start the pipeline
 
 NOW=$(date +"%Y-%m-%d-%H-%M-%S")
 
 echo "Starting pipeline with timestamp '${NOW}'";
+
+echo "Fetch the gene models from ${db}..."
 if [ -n "$password" ]
 then
-		bsub -q normal -o ${output_dir}/as_gff_${species}_${NOW}.out -e ${output_dir}/as_gff_${species}_${NOW}.err -J as_gff_${species}_${NOW} "perl Fetch_gff.pl -dbname ${db} -dbhost ${host} -dbport ${port} -dbuser ${user} -dbpass ${password} -o ${output_dir}/${species}_${NOW}_variants.gff"
+		perl Fetch_gff.pl -dbname ${db} -dbhost ${host} -dbport ${port} -dbuser ${user} -dbpass ${password} -o ${output_dir}/${species}_${NOW}_variants.gff
 else
-		bsub -q normal -o ${output_dir}/as_gff_${species}_${NOW}.out -e ${output_dir}/as_gff_${species}_${NOW}.err -J as_gff_${species}_${NOW} "perl Fetch_gff.pl -dbname ${db} -dbhost ${host} -dbport ${port} -dbuser ${user} -o ${output_dir}/${species}_${NOW}_variants.gff"
+		perl Fetch_gff.pl -dbname ${db} -dbhost ${host} -dbport ${port} -dbuser ${user} -o ${output_dir}/${species}_${NOW}_variants.gff
 fi
 
-bsub -q small -o ${output_dir}/as_compute_${species}_${NOW}.out -e ${output_dir}/as_compute_${species}_${NOW}.err -w "done(\"as_gff_${species}_${NOW}\")" -J as_compute_${species}_${NOW} "altSpliceFinder -i ${output_dir}/${species}_${NOW}_variants.gff -o ${output_dir}/${species}_${NOW}_events.gff --relax --statistics"
+echo "Compute the Alternative Splicing events";
+altSpliceFinder -i ${output_dir}/${species}_${NOW}_variants.gff -o ${output_dir}/${species}_${NOW}_events.gff --relax --statistics
 
+echo "Populate ${db} with alternative splicing information";
 if [ -n "$password" ]
 then
-bsub -q normal -o ${output_dir}/as_populate_${species}_${NOW}.out -e ${output_dir}/as_populate_${species}_${NOW}.err -w "done(\"as_compute_${species}_${NOW}\")" -J as_populate_${species}_${NOW} "perl load_alt_splice_gff.pl -file ${output_dir}/${species}_${NOW}_events.gff -host ${host} -user ${user} -pass ${password} -dbname ${core}"
+		perl load_alt_splice_gff.pl -file ${output_dir}/${species}_${NOW}_events.gff -host ${host} -user ${user} -pass ${password} -dbname ${db}
 else 
 		echo "Sorry, you did not provide any password. The script can't populate the database with the Alternative splicing information.";
 		echo "However, the results are available in ${output_dir}/${species}_${NOW}_events.gff";
 fi
 
-
+echo "All done."
+exit 0;